This is exactly what I was thinking with the proposed file structure, but perhaps we could organize it differently, there are many solutions so we can provide a scaffold via a ‘build your own’ (think modularity like legos), and then the 'plug 'n play section can be just that, I do however think that it is important to group things by Liquid Handling function because then the user is more readily able to use more of the code instead of having to go and dig through files for code that supposedly conveys the same protocol idea.
For Example, If a user were to come up with an elegant solution to a golden gate plasmid mapping, and it was more efficient than simply using a single pipet tip, then that should be shared, but if it is only in one section, it might be missed. I say that because there will be no true librarian of the aP library, and if people are going to add their own protocols, then it might be hard to find adjacent protocols and efficiently transfer information if they are not group via LH function.